I realise your girlfriend is MtF, but as a pre-T, FtM, newly-out guy I thought maybe an alternative perspective on transitioning might be helpful. I recently started using the bathroom of my identified gender, but not without freezing and bailing last minute for several weeks beforehand, worried that I wouldn't pass enough to "fit in" and not risk my safety.
If your girlfriend is still uncomfortable using the women's restroom, I can't recommend pushing it (to the point of discomfort for her, I mean). Personally, mentally transitioning was primarily hindered by my fear of binary gender presentation and wondering if I hit the mark. Perhaps she feels a similar societal pressure? Going in with her at first might help a lot; I only wish I'd had a guy friend I could have done that with, if only for the first time.
Whatever the case/decision, I wish you and your girlfriend the best of luck and a great college experience!